메뉴 건너뛰기




Volumn 2, Issue 9, 2007, Pages

Preference of small molecules for local minimum conformations when binding to proteins

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN STRUCTURE; VIRTUAL REALITY; CONFORMATION; METABOLISM; REPRODUCIBILITY; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 40749129010     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000820     Document Type: Article
Times cited : (38)

References (27)
  • 1
    • 33750639677 scopus 로고
    • The key-lock theory and the induced fit theory
    • Koshland DE (1995) The key-lock theory and the induced fit theory. Angew Chem Int Ed Engl 33: 2375-2378.
    • (1995) Angew Chem Int Ed Engl , vol.33 , pp. 2375-2378
    • Koshland, D.E.1
  • 2
    • 0019790028 scopus 로고
    • Conformational changes and drug action
    • Burgen AS (1981) Conformational changes and drug action. Fed Proc 40: 2723-2728.
    • (1981) Fed Proc , vol.40 , pp. 2723-2728
    • Burgen, A.S.1
  • 3
    • 0029976453 scopus 로고    scopus 로고
    • Conformational induction versus conformational selection: Evidence from allosteric enhancers
    • Bruns RF (1996) Conformational induction versus conformational selection: evidence from allosteric enhancers. Trends Pharmacol Sci 17: 189.
    • (1996) Trends Pharmacol Sci , vol.17 , pp. 189
    • Bruns, R.F.1
  • 4
    • 0029976454 scopus 로고    scopus 로고
    • Receptor conformational induction versus selection: All part of the same energy landscape, agonists can differentially stabilize multiple active states of receptors
    • Kenakin T (1996) Receptor conformational induction versus selection: all part of the same energy landscape, agonists can differentially stabilize multiple active states of receptors. Trends Pharmacol Sci 17: 190-191.
    • (1996) Trends Pharmacol Sci , vol.17 , pp. 190-191
    • Kenakin, T.1
  • 5
    • 10344237290 scopus 로고    scopus 로고
    • Docking studies on the complexed and uncomplexed FKBP12 structures with bound and unbound ligands: An implication of conformational selection mechanism for binding
    • Pang Y-P, Silva ND, Hydock C, Prendergast FG (1997) Docking studies on the complexed and uncomplexed FKBP12 structures with bound and unbound ligands: an implication of conformational selection mechanism for binding. J Mol Model 3: 240-248.
    • (1997) J Mol Model , vol.3 , pp. 240-248
    • Pang, Y.-P.1    Silva, N.D.2    Hydock, C.3    Prendergast, F.G.4
  • 6
    • 0035976367 scopus 로고    scopus 로고
    • EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
    • Pang Y-F, Perola E, Xu K, Prendergast FG (2001) EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J Comput Chem 22: 1750-1771.
    • (2001) J Comput Chem , vol.22 , pp. 1750-1771
    • Pang, Y.-F.1    Perola, E.2    Xu, K.3    Prendergast, F.G.4
  • 7
    • 33845971492 scopus 로고    scopus 로고
    • In silico drug discovery: Solving the "target-rich and lead-poor" imbalance using the genome-to-drug-lead paradigm
    • Pang Y-P (2007) In silico drug discovery: solving the "target-rich and lead-poor" imbalance using the genome-to-drug-lead paradigm. Clin Pharmacol Ther 81: 30-34.
    • (2007) Clin Pharmacol Ther , vol.81 , pp. 30-34
    • Pang, Y.-P.1
  • 8
    • 40749121259 scopus 로고    scopus 로고
    • EUDOC on Blue Gene: Accelerating the transfer of drug discoveries from laboratory to patient
    • in press
    • Pang Y-P, Mullins T, Swartz B, McAllister J, Smith B, et al. (2007) EUDOC on Blue Gene: accelerating the transfer of drug discoveries from laboratory to patient. IBM J Res Dev in press.
    • (2007) IBM J Res Dev
    • Pang, Y.-P.1    Mullins, T.2    Swartz, B.3    McAllister, J.4    Smith, B.5
  • 9
    • 0026425975 scopus 로고
    • Rusting of the lock and key model for protein-ligand binding
    • Jorgensen WL (1991) Rusting of the lock and key model for protein-ligand binding. Science 254: 954-955.
    • (1991) Science , vol.254 , pp. 954-955
    • Jorgensen, W.L.1
  • 10
    • 0032197018 scopus 로고    scopus 로고
    • Do active site conformations of small ligands correspond to low free-energy solution structures?
    • Vieth M, Hirst JD, Brooks III CL (1998) Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput-Aided Mol Design 12: 563-572.
    • (1998) J Comput-Aided Mol Design , vol.12 , pp. 563-572
    • Vieth, M.1    Hirst, J.D.2    Brooks III, C.L.3
  • 13
    • 2342586724 scopus 로고    scopus 로고
    • Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
    • Perola K, Charifson PS (2004) Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 47: 2499-2510.
    • (2004) J Med Chem , vol.47 , pp. 2499-2510
    • Perola, K.1    Charifson, P.S.2
  • 15
    • 41049115339 scopus 로고    scopus 로고
    • Case D (1999) Rigidity theory and applications; Thorpe M, Duxbury P, eds. New York: Kluwer Academic/Plenum Publishers. pp 329-344
    • Case D (1999) Rigidity theory and applications; Thorpe M, Duxbury P, eds. New York: Kluwer Academic/Plenum Publishers. pp 329-344.
  • 18
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell WD, Cieplak P, Bayly CI, Gould TR, Merz Jr KM, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
    • (1995) J Am Chem Soc , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, T.R.4    Merz Jr, K.M.5
  • 20
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham III TE, et al. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91: 1-41.
    • (1995) Comput Phys Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham III, T.E.5
  • 21
    • 0036829172 scopus 로고    scopus 로고
    • Structure ofthe Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein
    • Pornillos O, Alam SL, Davis DR, Sundquist WI (2002) Structure ofthe Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein. Nat Struct Biol 9: 812-817.
    • (2002) Nat Struct Biol , vol.9 , pp. 812-817
    • Pornillos, O.1    Alam, S.L.2    Davis, D.R.3    Sundquist, W.I.4
  • 22
    • 30344480804 scopus 로고    scopus 로고
    • From genome to drug lead: Identification of a small-molecule inhibitor of the SARS virus
    • Dooley AJ, Shindo N, Iaggart B, Park JG, Pang Y-P (2006) From genome to drug lead: identification of a small-molecule inhibitor of the SARS virus. Bioorg Med Chem Lett 16: 830-833.
    • (2006) Bioorg Med Chem Lett , vol.16 , pp. 830-833
    • Dooley, A.J.1    Shindo, N.2    Iaggart, B.3    Park, J.G.4    Pang, Y.-P.5
  • 23
    • 10344222619 scopus 로고    scopus 로고
    • Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: Catalytic efficiency regulated by substrate binding
    • Pang Y-P (2004) Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding. Proteins 57: 747-757.
    • (2004) Proteins , vol.57 , pp. 747-757
    • Pang, Y.-P.1
  • 24
    • 40749159291 scopus 로고    scopus 로고
    • Wang Q, Pang.Y-P (2007) Accurate reproduction of 161 small-molecule complex crystal structures using the EUDOG program: expanding the use of EUDOC to supramolecular chemistry. PLoS ONE 2: e531.
    • Wang Q, Pang.Y-P (2007) Accurate reproduction of 161 small-molecule complex crystal structures using the EUDOG program: expanding the use of EUDOC to supramolecular chemistry. PLoS ONE 2: e531.
  • 26
    • 84986516411 scopus 로고
    • Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
    • Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. J Comput Chem 16: 1357-1377.
    • (1995) J Comput Chem , vol.16 , pp. 1357-1377
    • Cieplak, P.1    Cornell, W.D.2    Bayly, C.3    Kollman, P.A.4
  • 27
    • 41049112081 scopus 로고    scopus 로고
    • Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Hohnson BG, et al. (1999) GAUSSIAN 98, Revision A.7. Gaussian, Inc. Pittsburgh, PA.
    • Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Hohnson BG, et al. (1999) GAUSSIAN 98, Revision A.7. Gaussian, Inc. Pittsburgh, PA.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.